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MFD_BACSU_1_450-UVRA_BACSU_121_263

Genes: A B A+B
Length: 450 143 575
Sequences: 9935 7073 3653
Seq/Len: 22.08 49.46 6.35
MirrorTree (Pazo et al. 2001) 0.10
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.

Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.04 1.75
2 0.00 0.04 2.09
5 0.00 0.04 2.51
10 0.00 0.04 2.80
20 0.00 0.04 2.98
100 0.01 0.04 3.60
0.09 0.04 6.16
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!

GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution.
Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
147_D 92_K 1.57 0.99 0.90
198_D 90_V 1.20 0.95 0.68
180_I 57_V 1.08 0.90 0.56
179_G 88_R 1.05 0.88 0.52
197_F 88_R 1.02 0.86 0.49
202_D 88_R 0.87 0.72 0.33
197_F 58_R 0.87 0.71 0.32
187_T 17_M 0.84 0.67 0.29
202_D 58_R 0.79 0.60 0.24
198_D 88_R 0.77 0.57 0.22
182_D 101_D 0.73 0.52 0.19
217_T 69_S 0.72 0.50 0.18
151_D 97_A 0.67 0.43 0.14
410_V 82_I 0.67 0.42 0.14
179_G 58_R 0.66 0.41 0.14
177_R 105_T 0.65 0.40 0.13
147_D 27_R 0.63 0.37 0.12
200_E 58_R 0.63 0.37 0.12
350_Q 63_G 0.63 0.36 0.12
267_I 110_G 0.60 0.33 0.10
210_D 104_E 0.60 0.32 0.10
76_D 26_E 0.59 0.31 0.09
198_D 92_K 0.58 0.30 0.09
355_E 36_I 0.58 0.30 0.09
199_T 92_K 0.56 0.28 0.08
219_T 61_I 0.56 0.28 0.08
200_E 88_R 0.56 0.27 0.08
199_T 88_R 0.56 0.27 0.08
387_Q 29_K 0.55 0.27 0.08
198_D 9_I 0.55 0.26 0.07
409_T 131_A 0.55 0.26 0.07
187_T 137_F 0.55 0.26 0.07
177_R 88_R 0.54 0.26 0.07
57_T 16_Q 0.54 0.26 0.07
200_E 64_E 0.54 0.25 0.07
224_G 100_S 0.54 0.25 0.07
274_L 129_H 0.54 0.25 0.07
404_K 82_I 0.53 0.24 0.07
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)

ID Seq/Len Name Options I_Prob Status
7103 2.9 MFD_BACSU_1_450-UVRA_BACSU_121_263 Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.41 Done - Shared
7102 1.81 MFD_BACSU_1_450-UVRA_BACSU_121_263 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
7091 6.35 MFD_BACSU_1_450-UVRA_BACSU_121_263 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.90 Done - Shared

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